Tim Hubbard

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Tim Hubbard
Tim Hubbard (8243443127).jpg
Born Timothy John Phillip Hubbard
Fields
Institutions
Alma mater
Thesis The design, expression and characterisation of a novel protein (1988)
Doctoral advisor Tom Blundell
Doctoral students
Known for
Website

Timothy John Phillip Hubbard is a Professor of Bioinformatics at King's College London, Head of Bioinformatics at Genomics England and Honorary Faculty at the Wellcome Trust Sanger Institute in Cambridge, UK.[2][23][24][25][26][27][28]

Education[edit]

Hubbard was educated at the University of Cambridge where he was awarded a Bachelor of Arts degree in Natural Sciences (Biochemistry) in 1985. He went on to do research in protein design in the Department of Crystallography, Birkbeck College, London where he was awarded a PhD in 1988[29] for research supervised by Tom Blundell.

Research and Career[edit]

Hubbard's research interests are in Bioinformatics, Computational biology and Genome Informatics.[1] During his tenure at WTSI he supervised several successful PhD students to completion in these areas of research.[4][6][8][10][12][14]

Hubbard was appointed Professor of Bioinformatics at King's in October 2013.[31] His research has been published in leading peer reviewed scientific journals including Nature,[32][33][34] the Journal of Molecular Biology,[18][35] Nucleic Acids Research,[20][21] Genome Biology,[19] Nature Methods,[36] Nature Reviews Cancer[37] and Bioinformatics.[38] His research been funded by the Medical Research Council (MRC) and the Biotechnology and Biological Sciences Research Council (BBSRC).[39]

References[edit]

  1. ^ a b Tim Hubbard's publications indexed by Google Scholar, a free service provided by Google
  2. ^ a b "Genomics England publishes results of its annotation assessment". Genomics England. 2014. Archived from the original on 2015-01-12. 
  3. ^ "Jong Bhak CV". jongbhak.com. Archived from the original on 2009-12-04. 
  4. ^ a b Brosch, Markus (2010). Development of computational methods for analysing proteomic data for genome annotation (PhD thesis). University of Cambridge. OCLC 890149364. 
  5. ^ Brosch, M; Saunders, G. I.; Frankish, A; Collins, M. O.; Yu, L; Wright, J; Verstraten, R; Adams, D. J.; Harrow, J; Choudhary, J. S.; Hubbard, T (2011). "Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome". Genome Research 21 (5): 756–67. doi:10.1101/gr.114272.110. PMC 3083093. PMID 21460061. 
  6. ^ a b Down, Thomas Alexander (2004). Computational localization of promoters and transcription start sites in mammalian genomes (PhD thesis). University of Cambridge. 
  7. ^ Down, T. A.; Hubbard, T. J. (2002). "Computational detection and location of transcription start sites in mammalian genomic DNA". Genome Research 12 (3): 458–61. doi:10.1101/gr.216102. PMC 155284. PMID 11875034. 
  8. ^ a b Doğruel, Mutlu (2008). Motif based computational identification of protein subcellular localisation (PhD thesis). University of Cambridge. OCLC 890154619. 
  9. ^ Doğruel, M; Down, T. A.; Hubbard, T. J. (2008). "NestedMICA as an ab initio protein motif discovery tool". BMC Bioinformatics 9: 19. doi:10.1186/1471-2105-9-19. PMC 2267705. PMID 18194537. 
  10. ^ a b Mattison, Jenny (2009). Analysis of genome-wide, cancer-associated mutation datasets in mouse and human (PhD thesis). University of Cambridge. OCLC 890152898. 
  11. ^ Mattison, J; Van Der Weyden, L; Hubbard, T; Adams, D. J. (2009). "Cancer gene discovery in mouse and man". Biochimica et Biophysica Acta (BBA) - Reviews on Cancer 1796 (2): 140–61. doi:10.1016/j.bbcan.2009.03.001. PMC 2756404. PMID 19285540. 
  12. ^ a b Piipari, Matias (2011). Inference and classification of eukaryotic cis-regulatory motifs (PhD thesis). University of Cambridge. 
  13. ^ Piipari, M; Down, T. A.; Saini, H; Enright, A; Hubbard, T. J. (2010). "I Motifs: An integrated sequence motif visualization and analysis environment". Bioinformatics 26 (6): 843–4. doi:10.1093/bioinformatics/btq026. PMC 2832821. PMID 20106815. 
  14. ^ a b Pocock, Matthew Richard (2004). Computational analysis of genomes (PhD thesis). University of Cambridge. OCLC 890159072. 
  15. ^ Pocock, M. R.; Hubbard, T. J. (2000). "A browser for expression data". Bioinformatics (Oxford, England) 16 (4): 402–3. PMID 10869040. 
  16. ^ Pocock, M. R.; Hubbard, T; Birney, E (1998). "SPEM: A parser for EMBL style flat file database entries". Bioinformatics (Oxford, England) 14 (9): 823–4. PMID 9918956. 
  17. ^ "Sanger Staff PhD theses". Wellcome Trust Sanger Institute. Archived from Sanger the original on 2015-04-07. 
  18. ^ a b Murzin, A. G.; Brenner, S.; Hubbard, T.; Chothia, C. (1995). "SCOP: A structural classification of proteins database for the investigation of sequences and structures" (PDF). Journal of Molecular Biology 247 (4): 536–540. doi:10.1016/S0022-2836(05)80134-2. PMID 7723011. 
  19. ^ a b Harrow, J; Denoeud, F; Frankish, A; Reymond, A; Chen, C. K.; Chrast, J; Lagarde, J; Gilbert, J. G.; Storey, R; Swarbreck, D; Rossier, C; Ucla, C; Hubbard, T; Antonarakis, S. E.; Guigo, R (2006). "GENCODE: Producing a reference annotation for ENCODE". Genome Biology. 7 Suppl 1: S4.1–9. doi:10.1186/gb-2006-7-s1-s4. PMC 1810553. PMID 16925838. 
  20. ^ a b Hubbard, T.; Barker, D.; Birney, E.; Cameron, G.; Chen, Y.; Clark, L.; Cox, T.; Cuff, J.; Curwen, V.; Down, T.; Durbin, R.; Eyras, E.; Gilbert, J.; Hammond, M.; Huminiecki, L.; Kasprzyk, A.; Lehvaslaiho, H.; Lijnzaad, P.; Melsopp, C.; Mongin, E.; Pettett, R.; Pocock, M.; Potter, S.; Rust, A.; Schmidt, E.; Searle, S.; Slater, G.; Smith, J.; Spooner, W.; Stabenau, A. (2002). "The Ensembl genome database project". Nucleic Acids Research 30 (1): 38–41. doi:10.1093/nar/30.1.38. PMC 99161. PMID 11752248. 
  21. ^ a b Farrell, C. M.; O'Leary, N. A.; Harte, R. A.; Loveland, J. E.; Wilming, L. G.; Wallin, C.; Diekhans, M.; Barrell, D.; Searle, S. M. J.; Aken, B.; Hiatt, S. M.; Frankish, A.; Suner, M. -M.; Rajput, B.; Steward, C. A.; Brown, G. R.; Bennett, R.; Murphy, M.; Wu, W.; Kay, M. P.; Hart, J.; Rajan, J.; Weber, J.; Snow, C.; Riddick, L. D.; Hunt, T.; Webb, D.; Thomas, M.; Tamez, P.; Rangwala, S. H. (2013). "Current status and new features of the Consensus Coding Sequence database". Nucleic Acids Research 42: D865. doi:10.1093/nar/gkt1059. PMC 3965069. PMID 24217909. 
  22. ^ Moult, J; Hubbard, T; Fidelis, K; Pedersen, J. T. (1999). "Critical assessment of methods of protein structure prediction (CASP): Round III". Proteins. Suppl 3: 2–6. doi:10.1002/(sici)1097-0134(1999)37:3+<2::aid-prot2>3.3.co;2-u. PMID 10526346. 
  23. ^ Tim Hubbard on Twitter
  24. ^ Tim Hubbard's publications indexed by the Scopus bibliographic database, a service provided by Elsevier.
  25. ^ Tim Hubbard from the ACM Portal
  26. ^ Tim Hubbard's publications indexed by the DBLP Bibliography Server at the University of Trier
  27. ^ Hopkin, Karen (2009-10-01). "Tim Hubbard: Genome Guru". The Scientist. Archived from the original on 2014-03-04. 
  28. ^ Tim Hubbard publications from Europe PubMed Central
  29. ^ Hubbard, Tim (1988). The design, expression and characterisation of a novel protein (PhD thesis). University of London. Archived from the original on 2015-05-19. 
  30. ^ "Wellcome Trust Sanger Institute Honorary Faculty - Dr Tim Hubbard". Archived from the original on 2015-03-23. 
  31. ^ "Professor Tim Hubbard, King's College London". Archived from the original on 2014-02-23. 
  32. ^ ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET et al. (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature 447 (7146): 799–816. Bibcode:2007Natur.447..799B. doi:10.1038/nature05874. PMC 2212820. PMID 17571346. 
  33. ^ Lander, E. S.; Linton, M.; Birren, B.; Nusbaum, C.; Zody, C.; Baldwin, J.; Devon, K.; Dewar, K.; Doyle, M.; Fitzhugh, W.; Funke, R.; Gage, D.; Harris, K.; Heaford, A.; Howland, J.; Kann, L.; Lehoczky, J.; Levine, R.; McEwan, P.; McKernan, K.; Meldrim, J.; Mesirov, J. P.; Miranda, C.; Morris, W.; Naylor, J.; Raymond, C.; Rosetti, M.; Santos, R.; Sheridan, A. et al. (Feb 2001). "Initial sequencing and analysis of the human genome". Nature 409 (6822): 860–921. doi:10.1038/35057062. ISSN 0028-0836. PMID 11237011. 
  34. ^ Birney, E; Bateman, A; Clamp, M. E.; Hubbard, T. J. (2001). "Mining the draft human genome". Nature 409 (6822): 827–8. doi:10.1038/35057004. PMC 2658632. PMID 11236999. 
  35. ^ Park, J; Teichmann, S. A.; Hubbard, T; Chothia, C (1997). "Intermediate sequences increase the detection of homology between sequences". Journal of Molecular Biology 273 (1): 349–54. doi:10.1006/jmbi.1997.1288. PMID 9367767. 
  36. ^ Engström, P. R. G.; Steijger, T.; Sipos, B.; Grant, G. R.; Kahles, A.; Alioto, T.; Behr, J.; Bertone, P.; Bohnert, R.; Campagna, D.; Davis, C. A.; Dobin, A.; Engström, P. R. G.; Gingeras, T. R.; Goldman, N.; Grant, G. R.; Guigó, R.; Harrow, J.; Hubbard, T. J.; Jean, G. R.; Kahles, A.; Kosarev, P.; Li, S.; Liu, J.; Mason, C. E.; Molodtsov, V.; Ning, Z.; Ponstingl, H.; Prins, J. F.; Rätsch, G. (2013). "Systematic evaluation of spliced alignment programs for RNA-seq data". Nature Methods 10 (12): 1185. doi:10.1038/nmeth.2722. 
  37. ^ Futreal, P. A.; Coin, L; Marshall, M; Down, T; Hubbard, T; Wooster, R; Rahman, N; Stratton, M. R. (2004). "A census of human cancer genes". Nature Reviews Cancer 4 (3): 177–83. doi:10.1038/nrc1299. PMC 2665285. PMID 14993899. 
  38. ^ Reeves, G. A.; Eilbeck, K.; Magrane, M.; O'Donovan, C.; Montecchi-Palazzi, L.; Harris, M. A.; Orchard, S.; Jimenez, R. C.; Prlic, A.; Hubbard, T. J. P.; Hermjakob, H.; Thornton, J. M. (2008). "The Protein Feature Ontology: A tool for the unification of protein feature annotations". Bioinformatics 24 (23): 2767. doi:10.1093/bioinformatics/btn528. 
  39. ^ "UK Government Grants awarded to Tim Hubbard". Research Councils UK. Archived from the original on 2015-04-09.